Package: phylopred 0.1.0

Angel Robles

phylopred: Predicting Species Interactions from Phylogenetic Distance

Tools to model and predict host-parasite (and other pairwise species) interactions from phylogenetic distance under presence-only data. Provides pairwise host-sharing logistic models with cluster-aware bootstrap and slope comparison between clades, presence-only performance metrics (a threshold efficiency metric and a phylogenetic partial receiver operating characteristic (ROC) adapted from Peterson, Papes and Soberon (2008) <doi:10.1016/j.ecolmodel.2007.11.008>), positive-unlabeled host prediction, and leave-hosts-out validation. Methods build on Robles-Fernandez and Lira-Noriega (2017) <doi:10.3389/fams.2017.00017>.

Authors:Angel Robles [aut, cre]

phylopred_0.1.0.tar.gz
phylopred_0.1.0.zip(r-4.7-any)phylopred_0.1.0.zip(r-4.6-any)
phylopred_0.1.0.tar.gz(r-4.7-any)phylopred_0.1.0.tar.gz(r-4.6-any)
phylopred_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phylopred/json (API)

# Install 'phylopred' in R:
install.packages('phylopred', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/alrobles/phylopred/issues

Pkgdown/docs site:https://alrobles.github.io

Datasets:
  • beetleTreeInteractions - Beetle tree interaction table.
  • fish_tree - Phylogenetic tree of marine fish hosts of Caligus and Lepeophtheirus
  • phy_dist - Phylogenetic distance matrix among host data on phylopred

On CRAN:

Conda:

1.70 score 2 scripts 18 exports 21 dependencies

Last updated from:9e61e9447d. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develOK146
source / vignettesOK174
linux-releaseOK164
windows-develOK84
windows-releaseOK139
wasm-releaseOK118

Exports:align_phylopred_inputsbootstrap_phylopred_modelcluster_bootstrap_phylopredcompare_phylopred_slopesevaluate_phylopred_modelextract_phylopred_coefficientsfit_phylopred_modelfit_phylopred_puhost_specificity_indexhost_threshold_metricphylo_partial_rocphylopred_confidence_ellipsepoulin_stdpredict_phylopred_probabilityprepare_incidence_matrixprepare_pair_datataxonomic_step_matrixvalidate_host_prediction

Dependencies:clicodetoolsforeachglmnetglueiteratorslatticelifecyclemagrittrMatrixpillarpkgconfigRcppRcppEigenrlangshapesurvivaltibbleutf8vctrsxplus

Readme and manuals

Help Manual

Help pageTopics
Align incidence matrix and phylogenetic distance matrixalign_phylopred_inputs
Beetle tree interaction table.beetleTreeInteractions
Bootstrap a phylopred logistic regression modelbootstrap_phylopred_model
Cluster bootstrap for pairwise host-sharing modelscluster_bootstrap_phylopred
Compare host-sharing slopes between two cladescompare_phylopred_slopes
Evaluate the predictive capacity of a pairwise host-sharing modelevaluate_phylopred_model
Extract coefficients from a phylopred model or bootstrap objectextract_phylopred_coefficients
Phylogenetic tree of marine fish hosts of Caligus and Lepeophtheirusfish_tree
Fit a phylopred logistic regression modelfit_phylopred_model
Positive-unlabeled host prediction via xplus (PLUS algorithm)fit_phylopred_pu
Host specificity index (S_TD) for every parasite in an interaction tablehost_specificity_index
Threshold metric f_gamma for predicted host suitabilityhost_threshold_metric
Phylogenetic distance matrix among host data on phylopredphy_dist
Phylogenetic partial ROC (Peterson, Papes & Soberon 2008 analogue)phylo_partial_roc
Joint confidence ellipse for intercept and slopephylopred_confidence_ellipse
Poulin and Mouillot taxonomic/phylogenetic distinctness index (S_TD)poulin_std
Predict host susceptibility probabilities from logistic regression coefficientspredict_phylopred_probability
Prepare an incidence matrix from an interaction tableprepare_incidence_matrix
Build a pairwise host-sharing data set from an interaction tableprepare_pair_data
Build a taxonomic step-distance matrix (Poulin & Mouillot scale)taxonomic_step_matrix
Leave-hosts-out validation of host predictionsvalidate_host_prediction